# The MIT License (MIT)
# Copyright (c) 2017 Louise AC Millard, MRC Integrative Epidemiology Unit, University of Bristol
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
# documentation files (the "Software"), to deal in the Software without restriction, including without
# limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so, subject to the following
# conditions:
#
# The above copyright notice and this permission notice shall be included in all copies or substantial portions
# of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
# TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
# CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.


# Replace NaN and empty values with NA in pheno
replaceNaN <- function(pheno) {

	if (is.factor(pheno)) {
		
		phenoReplaced = pheno

		nanStr  = which(phenoReplaced=="NaN")
        	phenoReplaced[nanStr]=NA 
		
		emptyx  = which(phenoReplaced=="")
       		phenoReplaced[emptyx]=NA

	}
	else {

		phenoReplaced = pheno
		nanx  = which(is.nan(phenoReplaced))
		phenoReplaced[nanx] = NA;

		emptyStr  = which(phenoReplaced=="")	
		phenoReplaced[emptyStr] = NA;
	    
	}

	return(phenoReplaced)

}
